Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011045.1 Corchorus olitorius cultivar O-4 contig11078, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 741
Length: 1236
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Found at i:1022 original size:33 final size:33
Alignment explanation
Indices: 985--1236 Score: 138
Period size: 33 Copynumber: 7.2 Consensus size: 33
975 GTTGCCAAGC
985 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
1 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
**
1018 GCCATCGGCAAGTCCCGAGTGCCATCGGCAACTCCCGAGT
1 GCCATCGGCAAGTCCCGAGTG---T---CAA-GGCCGAGT
* * * *
1058 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGT
1 GCCATCGG-CAAGTCCCGAGT-GTCAAG-GCCGAGT
* * * *
1091 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGT
1 GCCATCGG-CAAGTCCCGAGT-GTCAAG-GCCGAGT
** *
1124 GCCATCGGCAAGTGTCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGGCAAGTCCCGAGTG---T---CAAG-GCCGAGT
*
1164 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGT
1 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
* *
1197 GCCATCAGCAAGTCCCGAGTGCCAAGGCCGAGT
1 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
1230 GCCATCG
1 GCCATCG
Statistics
Matches: 181, Mismatches: 19, Indels: 38
0.76 0.08 0.16
Matches are distributed among these distances:
33 117 0.65
34 8 0.04
35 1 0.01
36 1 0.01
38 1 0.01
39 7 0.04
40 46 0.25
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.15
Consensus pattern (33 bp):
GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
Found at i:1037 original size:20 final size:20
Alignment explanation
Indices: 1007--1187 Score: 185
Period size: 20 Copynumber: 9.8 Consensus size: 20
997 TCCCGAGTGT
1007 CAAG-GCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1026 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
* *
1046 CAACTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1060 CAAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1079 CAAGTGCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1093 CAAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1112 CAAGTGCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1132 CAAGTGTCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1152 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1172 CAAGTCCCGAGTGCCA
1 CAAGTGCCGAGTGCCA
1188 AGGCCGAGTG
Statistics
Matches: 136, Mismatches: 11, Indels: 29
0.77 0.06 0.16
Matches are distributed among these distances:
13 13 0.10
14 7 0.05
16 2 0.01
17 2 0.01
19 12 0.09
20 100 0.74
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (20 bp):
CAAGTGCCGAGTGCCATCGG
Found at i:1054 original size:53 final size:53
Alignment explanation
Indices: 985--1236 Score: 282
Period size: 53 Copynumber: 4.8 Consensus size: 53
975 GTTGCCAAGC
* *
985 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT
* *
1038 GCCATCGGCAACTCCCGAGTGCCAAGGCCTAGTGCCATCGGCAAGTGCCGAGT
1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT
* * * * *
1091 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGTGCCATCGGCAAGTGTCGAGT
1 GCCATCGG-CAAGTCCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAAGTGCCGAGT
* * * *
1144 GCCATCGGCAAGTCCCGAGTGCCATCGG-CAAGTCCCGAGT-GCCAAG-GCCGAGT
1 GCCATCGGCAAGTCCCGAGTGCCA-AGGCCGAGTGCC-A-TCGGCAAGTGCCGAGT
*
1197 GCCATCAGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCG
1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCG
Statistics
Matches: 164, Mismatches: 24, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
51 2 0.01
52 12 0.07
53 134 0.82
54 13 0.08
55 3 0.02
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.15
Consensus pattern (53 bp):
GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT
Found at i:1056 original size:40 final size:40
Alignment explanation
Indices: 1012--1187 Score: 182
Period size: 33 Copynumber: 4.8 Consensus size: 40
1002 AGTGTCAAGG
* *
1012 CCGAGTGCCATCGGCAAGTCCCGAGTGCCATCGGCAACTC
1 CCGAGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTC
* *
1052 CCGAGTG----C--CAAG-GCCTAGTGCCATCGGCAAGTG
1 CCGAGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTC
* *
1085 CCGAGTG----C--CAAG-GCCTAGTGCCATCGGCAAGTG
1 CCGAGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTC
*
1118 CCGAGTGCCATCGGCAAGTGTCGAGTGCCATCGGCAAGTC
1 CCGAGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTC
*
1158 CCGAGTGCCATCGGCAAGTCCCGAGTGCCA
1 CCGAGTGCCATCGGCAAGTGCCGAGTGCCA
1188 AGGCCGAGTG
Statistics
Matches: 120, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
33 57 0.47
34 4 0.03
36 1 0.01
37 1 0.01
39 4 0.03
40 53 0.44
ACGTcount: A:0.20, C:0.33, G:0.31, T:0.15
Consensus pattern (40 bp):
CCGAGTGCCATCGGCAAGTGCCGAGTGCCATCGGCAAGTC
Done.